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Bigelow Laboratory Single Cell Genomics Center

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About Bigelow Laboratory Single Cell Genomics Center

Type: Non Profit Divison of: Bigelow Laboratory for Ocean Sciences

SCGC® is a nonprofit research and service center at Bigelow Laboratory for Ocean Sciences, with its primary focus on microbial single cell genomics. Our mission is to make single cell genomics accessible to the broad research community and to serve as an engine for discoveries in microbial ecology, evolution,... Show more »

SCGC® is a nonprofit research and service center at Bigelow Laboratory for Ocean Sciences, with its primary focus on microbial single cell genomics. Our mission is to make single cell genomics accessible to the broad research community and to serve as an engine for discoveries in microbial ecology, evolution, bioprospecting and human health.

Single cell DNA sequencing, pioneered by SCGC® scientists, reads the genomic blueprints of the most fundamental units of life without the need for cultivation. This is a powerful approach to analyze biochemical properties and evolutionary histories of uncultured microorganisms, thought to constitute over 99% of biological diversity on Earth. Single cell genomics is also emerging as a revolutionary technology in the studies of cancer, autoimmune diseases and hereditary disorders.

SCGC® is the first shared user facility of its kind. Since its establishment in 2009, SCGC® developed partnerships and supported research projects at over 100 universities, research institutes, and companies in six continents. Over 1,000,000 individual cells have been processed through our high-throughput pipeline. Sources of these cells range from diverse marine environments, to soils, the deep subsurface, gut contents, and others. This has provided unique genomic data from many major evolutionary branches of bacteria, archaea, and eukarya that resist cultivation, making a significant impact on our understanding of life on our planet.

Although invisible to human eyes, unicellular microorganisms are the oldest, the most abundant, and the most diverse forms of life. Over 99% of microorganisms remain uncultured, making them inaccessible to many classical microbiology methods. Uncultured microorganisms dominate many functions of the biosphere, including the productivity of the oceans, the fertility of soils, the health of plants and animals, including humans, and the global cycles of carbon, nitrogen, and other elements. This “microbial uncultured majority” also harbors an enormous potential for novel natural product discovery and bioenergy production.

User fees are charged to cover SCGC® operational expenses. SCGC® equipment acquisition, infrastructure upgrades and initial method development have been supported, in part, by the U. S. National Science Foundation, the Department of Energy, the National Aeronautics and Space Administration, and the State of Maine Technology Institute.

List of SCGC services:
Service Cat # Unit Unit price*
SINGLE CELL ISOLATION AND WHOLE GENOME AMPLIFICATION
SAG Generation 2 S-201 384-well plate $3,800
SINGLE CELL DNA SEQUENCING AND BIOINFORMATICS
LoCoS™ – Low Coverage Sequencing S-202 384-well plate $15,000
Post-LoCoS™ WGS of prokaryotes** S-203 Up to 100 SAGs $15,000
Prokaryote SAG WGS, small batch S-015 10 SAGs $9,900
Prokaryote SAG WGS, medium batch S-016 48 SAGs $29,900
Eukaryote SAG WGS S-018 Flexible Req. a quote
ADDITIONAL SERVICES
SAG re-arraying S-105 96-well plate $450
Sample cryoprotectant glyTE S-019 10 mL $100
Consultation S-011 1 hour $260
Customized Services S-100 Req. a quote

*All prices are in US dollars (USD). Service fees do not include shipping costs. 15% discount is applied if more than 10 same items (catalog number) are ordered simultaneously. 15% discount is also applied if any combination of SCGC services that exceed $200,000 in value are ordered simultaneously. 20% discount is applied on all services for Bigelow Laboratory in-house projects.
** To be eligible for this service, all Illumina libraries must originate from a single SAG plate on which LoCoS™ (S-202) has already been performed. Furthermore, SAGs for which insufficient Illumina library quantities are produced during LoCoS™ (<0.2% of reads in a LoCoS™ set) are not eligible for this service.
NOTE: As of January 1, 2018, we no longer accept new requests for legacy services “SAG Generation 1” and PCR-based screens (S-101, S-102, S-103, S-104 and S-106). For a limited time, these services may be arranged for already ongoing SCGC projects.

COST ESTIMATE: CASE STUDY
Let’s assume that an external SCGC customer wants to a) generate one 384-well plate of prokaryote single amplified genomes (SAGs); b) perform a low coverage sequencing on this plate; and 3) perform deeper sequencing on 100 SAGs from the same plate. Fees for this work are summarized in Table 2. Deliverables include:

  1. One 384-well microplate containing SAGs with associated flow cytometry and gDNA amplification kinetics data

  2. Annotated genome sequences and QC of 100 deep-sequenced SAGs and associated metadata.

  3. Annotated genome sequences and QC of the remaining 217, LoCoS™-sequenced SAGs and associated metadata.

Table 2. Cost estimate for a hypothetical SCGC project.

Service Cat. # Unit Price per unit # of units Amount
SAG Generation 2 S-201 384-well plate $3,800 1 $3,800
LoCoS™ – Low Coverage Sequencing S-202 384-well plate $15,000 1 $15,000
Post-LoCoS™ WGS of prokaryotes S-203 Up to 100 SAGs $15,000 1 $15,000
Total $33,800

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Our Services (16)


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Single Amplified Genome (SAG) Generation

Starting at $3,800.00 per unit

SINGLE CELL ISOLATION AND WHOLE GENOME AMPLIFICATION- SAG Generation 2 (S-201)

Starting at $3,800.00 per unit

Single amplified genomes (SAGs) are whole genome amplification products obtained from individual cells or individual particles of DNA viruses. They can be used in similar ways to DNA extracts from pure... Show more »

SINGLE CELL ISOLATION AND WHOLE GENOME AMPLIFICATION- SAG Generation 2 (S-201)

Starting at $3,800.00 per unit

Single amplified genomes (SAGs) are whole genome amplification products obtained from individual cells or individual particles of DNA viruses. They can be used in similar ways to DNA extracts from pure cultures. The S-201 service includes separation of individual cells or DNA-containing viral particles into wells of a 384-well plate by fluorescence-activated cell sorting (FACS), followed by cell lysis with KOH and genomic DNA amplification by WGA-X, a new method developed at SCGC. Compared to the earlier, multiple displacement amplification technique, WGA-X improves average genome recovery from individual cells and viral particles, with most notable enhancements observed in SAGs with high G+C content. Deliverables of S-201 include: a) one 384-well microplate containing single cell or viral particle WGA-X products, 10 uL per well, usually averaging 1 microgram gDNA per well; b) index FACS data files; and c) WGA-X kinetics data obtained by measuring fluorescence of a DNA stain. One row and three columns of positive and negative controls are included in each 384-well microplate. For a standard S-201 service fee to be applicable, the following conditions must be met:

  1. Cells or viruses are in aquatic solution, are less than 100 micrometers in diameter, and are cryopreserved and shipped following SCGC recommendations (see Preparation and Shipment on SCGC website). Only particles <40 micrometers in diameter can be sorted in index FACS mode.
  2. Cell or viral sorting is based on SYTO-9 fluorescence (provided by SCGC), particle autofluorescence, or probes that are applied by SCGC customer prior to shipping to SCGC.
  3. Only one sample is used per microplate, following SCGC’s standard plate setup.
    Samples that have not been brought into aquatic suspension by SCGC customers may also be analyzed as a customized service. Please contact SCGC manager Brian Thompson for additional advice on how to produce SCGC-compatible samples in your own lab or for a feasibility assessment and a quote.
    SAG generation success varies among samples and depends on many factors, such as: a) preservation of intact cells and gDNA prior to cell sorting; b) successful discrimination of cells and viral particles from other particles during FACS; and c) successful single cell lysis and DNA amplification. Please note that viral particles may be particularly difficult to discriminate from other DNA-containing particles in sub-cellular size range when working with non-aquatic samples.
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Single Cell DNA Sequencing

Starting at $9,900.00 per unit

SINGLE CELL DNA SEQUENCING AND BIOINFORMATICS- LoCoS™ – Low Coverage Sequencing (S-202)

Starting at $15,000.00 per unit

SCGC developed LoCoS™ in order to retrieve some genomic information from most SAGs on a 384-well plate at a minimal cost, currently under $50 per genome. Deliverables include: a) original, 2×150 bp... Show more »

SINGLE CELL DNA SEQUENCING AND BIOINFORMATICS- LoCoS™ – Low Coverage Sequencing (S-202)

Starting at $15,000.00 per unit

SCGC developed LoCoS™ in order to retrieve some genomic information from most SAGs on a 384-well plate at a minimal cost, currently under $50 per genome. Deliverables include: a) original, 2×150 bp sequence reads (number per SAG is variable, average around 300,000), assembled contigs, assembly statistics, functional annotation by Prokka, taxonomic assignments based on checkM and SSU rRNA gene phylogeny, and QC. Please note that the obtained sequencing depth is highly variable among SAGs and is not sufficient for high-quality genome recovery from most SAGs. Therefore S-202 should be considered primarily as an initial screen of SAGs, to be followed by deeper sequencing (e.g. SCGC services S-203, S-015, S-016 or S-018). Further information on LoCoS™ and research examples are available in Stepanauskas et al. (2017).

SINGLE CELL DNA SEQUENCING AND BIOINFORMATICS- Post-LoCoS™ WGS of prokaryotes (S-203)

Starting at $15,000.00 per unit

This service includes deeper sequencing, de novo assembly and functional annotation of up to 100 Illumina libraries that have already been produced, in sufficient quantity, by an S-202 service from a single SAG plate. The total number of 2×150 bp reads produced by this service is around 400 million and is distributed about equally among the selected SAGs. Thus, the sequencing depth of each SAG depends on the number of SAGs selected for this service. Larger number of reads per SAG usually results in better genome recovery, but this relationship is not linear.

Please note that, in order to be eligible for this service, all Illumina libraries must originate from a single SAG plate on which LoCoS™ (S-202) has already been performed. Furthermore, SAGs for which insufficient Illumina library quantities are produced during LoCoS™ (<0.2% of all LoCoS™ reads from a SAG plate) are not eligible for this service. Other SAGs can be sequenced using SCGC services S-015, S-016 or S-018. Per customer’s request, SCGC can generate lists of SAGs that meet S-203 eligibility criteria. Please note that, due to potential liquid handling inconsistencies, some SAGs may receive insufficient numbers of sequence reads. Due to its high-throughput, low-cost nature, service S-203 does not include free re-sequencing of such SAGs, unless the number of affected SAGs exceeds 10 per plate.

Please note that genome recovery from SAGs is variable and ranges from 0% to 100%. Incomplete genome recovery may be caused by diverse factors, such as DNA degradation due to viral infections or handling prior to sorting, incomplete cell lysis, DNA interactions with other cellular components, amplification and sequencing biases, and others. If multiple, closely related SAGs of interest are available, the following strategies may improve the probability of high genome recovery: a) sequencing SAGs with lowest WGA-X or MDA Cp values; and b) sequencing multiple, related SAGs for a population-level genome content analysis.

SINGLE CELL DNA SEQUENCING AND BIOINFORMATICS- Prokaryote SAG WGS, small batch- 10 SAGs (S-015)

Starting at $9,900.00 per unit

These services include preparation of Illumina libraries, sequencing of at least 3 million 2×150 bp reads per SAG, de novo assembly and functional annotation and QC of each SAG. Deliverables include original sequence reads, assembled contigs, assembly statistics, annotation by Prokka, taxonomic assignments based on checkM and SSU rRNA gene phylogeny, and the output of various QC steps. In difference to S-203, each service request may contain SAGs from multiple plates and there is no requirement for S-202 being done first.

Please note that genome recovery from SAGs is variable and ranges from 0% to 100%. Incomplete genome recovery may be caused by diverse factors, such as DNA degradation due to viral infections or handling prior to sorting, incomplete cell lysis, DNA interactions with other cellular components, amplification and sequencing biases, and others. If multiple, closely related SAGs of interest are available, the following strategies may significantly improve the probability of high genome recovery: a) sequencing SAGs with lowest WGA-X or MDA Cp values; and b) sequencing multiple, related SAGs for a population-level genome content analysis.

SINGLE CELL DNA SEQUENCING AND BIOINFORMATICS- Prokaryote SAG WGS, medium batch- 48 SAGs (S-016)

Starting at $29,900.00 per unit

These services include preparation of Illumina libraries, sequencing of at least 3 million 2×150 bp reads per SAG, de novo assembly and functional annotation and QC of each SAG. Deliverables include original sequence reads, assembled contigs, assembly statistics, annotation by Prokka, taxonomic assignments based on checkM and SSU rRNA gene phylogeny, and the output of various QC steps. In difference to S-203, each service request may contain SAGs from multiple plates and there is no requirement for S-202 being done first.

Please note that genome recovery from SAGs is variable and ranges from 0% to 100%. Incomplete genome recovery may be caused by diverse factors, such as DNA degradation due to viral infections or handling prior to sorting, incomplete cell lysis, DNA interactions with other cellular components, amplification and sequencing biases, and others. If multiple, closely related SAGs of interest are available, the following strategies may significantly improve the probability of high genome recovery: a) sequencing SAGs with lowest WGA-X or MDA Cp values; and b) sequencing multiple, related SAGs for a population-level genome content analysis.

SINGLE CELL DNA SEQUENCING AND BIOINFORMATICS- Eukaryote SAG WGS (S-018)

Price on request

This service includes preparation of Illumina libraries, sequencing and de novo assembly of eukaryote SAGs. Deliverables include original sequence reads, assembled contigs, assembly statistics, taxonomic assignments based on SSU rRNA gene phylogeny, and QC. Genome annotation is not included in this service. If no greater sequencing depth than for prokaryotes is desired, then the fees are identical as for prokaryote SAG WGS (see S-202, S-203, S-015 and S-016). However, due to the highly variable and generally larger than prokaryote genome sizes of eukaryotes, greater sequencing effort may be needed for a comparable genome fraction to be recovered, in which case the fee for this service depends on the desired sequencing effort.

As with prokaryotes (see above), the fraction of a genome recovered from each eukaryote SAG is variable. Benchmarking of SCGC’s workflow on two marine algae demonstrated high data quality, with the frequency of assembly artifacts that is comparable to those in prokaryote SAGs. However, please note that SPAdes, which we use in de novo assemblies, has not been optimized for diploid organisms. Furthermore, we have not tested the performance of our de novo assembly pipeline on genomes larger than 32 Mbp and therefore cannot guarantee the provision of such assemblies.

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Single Cell Sequencing Data Analysis

Starting at $9,900.00 per unit

SINGLE CELL DNA SEQUENCING AND BIOINFORMATICS- LoCoS™ – Low Coverage Sequencing (S-202)

Starting at $15,000.00 per unit

SCGC developed LoCoS™ in order to retrieve some genomic information from most SAGs on a 384-well plate at a minimal cost, currently under $50 per genome. Deliverables include: a) original, 2×150 bp... Show more »

SINGLE CELL DNA SEQUENCING AND BIOINFORMATICS- LoCoS™ – Low Coverage Sequencing (S-202)

Starting at $15,000.00 per unit

SCGC developed LoCoS™ in order to retrieve some genomic information from most SAGs on a 384-well plate at a minimal cost, currently under $50 per genome. Deliverables include: a) original, 2×150 bp sequence reads (number per SAG is variable, average around 300,000), assembled contigs, assembly statistics, functional annotation by Prokka, taxonomic assignments based on checkM and SSU rRNA gene phylogeny, and QC. Please note that the obtained sequencing depth is highly variable among SAGs and is not sufficient for high-quality genome recovery from most SAGs. Therefore S-202 should be considered primarily as an initial screen of SAGs, to be followed by deeper sequencing (e.g. SCGC services S-203, S-015, S-016 or S-018). Further information on LoCoS™ and research examples are available in Stepanauskas et al. (2017).

SINGLE CELL DNA SEQUENCING AND BIOINFORMATICS- Post-LoCoS™ WGS of prokaryotes (S-203)

Starting at $15,000.00 per unit

This service includes deeper sequencing, de novo assembly and functional annotation of up to 100 Illumina libraries that have already been produced, in sufficient quantity, by an S-202 service from a single SAG plate. The total number of 2×150 bp reads produced by this service is around 400 million and is distributed about equally among the selected SAGs. Thus, the sequencing depth of each SAG depends on the number of SAGs selected for this service. Larger number of reads per SAG usually results in better genome recovery, but this relationship is not linear.

Please note that, in order to be eligible for this service, all Illumina libraries must originate from a single SAG plate on which LoCoS™ (S-202) has already been performed. Furthermore, SAGs for which insufficient Illumina library quantities are produced during LoCoS™ (<0.2% of all LoCoS™ reads from a SAG plate) are not eligible for this service. Other SAGs can be sequenced using SCGC services S-015, S-016 or S-018. Per customer’s request, SCGC can generate lists of SAGs that meet S-203 eligibility criteria. Please note that, due to potential liquid handling inconsistencies, some SAGs may receive insufficient numbers of sequence reads. Due to its high-throughput, low-cost nature, service S-203 does not include free re-sequencing of such SAGs, unless the number of affected SAGs exceeds 10 per plate.

Please note that genome recovery from SAGs is variable and ranges from 0% to 100%. Incomplete genome recovery may be caused by diverse factors, such as DNA degradation due to viral infections or handling prior to sorting, incomplete cell lysis, DNA interactions with other cellular components, amplification and sequencing biases, and others. If multiple, closely related SAGs of interest are available, the following strategies may improve the probability of high genome recovery: a) sequencing SAGs with lowest WGA-X or MDA Cp values; and b) sequencing multiple, related SAGs for a population-level genome content analysis.

SINGLE CELL DNA SEQUENCING AND BIOINFORMATICS- Prokaryote SAG WGS, small batch- 10 SAGs (S-015)

Starting at $9,900.00 per unit

These services include preparation of Illumina libraries, sequencing of at least 3 million 2×150 bp reads per SAG, de novo assembly and functional annotation and QC of each SAG. Deliverables include original sequence reads, assembled contigs, assembly statistics, annotation by Prokka, taxonomic assignments based on checkM and SSU rRNA gene phylogeny, and the output of various QC steps. In difference to S-203, each service request may contain SAGs from multiple plates and there is no requirement for S-202 being done first.

Please note that genome recovery from SAGs is variable and ranges from 0% to 100%. Incomplete genome recovery may be caused by diverse factors, such as DNA degradation due to viral infections or handling prior to sorting, incomplete cell lysis, DNA interactions with other cellular components, amplification and sequencing biases, and others. If multiple, closely related SAGs of interest are available, the following strategies may significantly improve the probability of high genome recovery: a) sequencing SAGs with lowest WGA-X or MDA Cp values; and b) sequencing multiple, related SAGs for a population-level genome content analysis.

SINGLE CELL DNA SEQUENCING AND BIOINFORMATICS- Prokaryote SAG WGS, medium batch- 48 SAGs (S-016)

Starting at $29,900.00 per unit

These services include preparation of Illumina libraries, sequencing of at least 3 million 2×150 bp reads per SAG, de novo assembly and functional annotation and QC of each SAG. Deliverables include original sequence reads, assembled contigs, assembly statistics, annotation by Prokka, taxonomic assignments based on checkM and SSU rRNA gene phylogeny, and the output of various QC steps. In difference to S-203, each service request may contain SAGs from multiple plates and there is no requirement for S-202 being done first.

Please note that genome recovery from SAGs is variable and ranges from 0% to 100%. Incomplete genome recovery may be caused by diverse factors, such as DNA degradation due to viral infections or handling prior to sorting, incomplete cell lysis, DNA interactions with other cellular components, amplification and sequencing biases, and others. If multiple, closely related SAGs of interest are available, the following strategies may significantly improve the probability of high genome recovery: a) sequencing SAGs with lowest WGA-X or MDA Cp values; and b) sequencing multiple, related SAGs for a population-level genome content analysis.

SINGLE CELL DNA SEQUENCING AND BIOINFORMATICS- Eukaryote SAG WGS (S-018)

Price on request

This service includes preparation of Illumina libraries, sequencing and de novo assembly of eukaryote SAGs. Deliverables include original sequence reads, assembled contigs, assembly statistics, taxonomic assignments based on SSU rRNA gene phylogeny, and QC. Genome annotation is not included in this service. If no greater sequencing depth than for prokaryotes is desired, then the fees are identical as for prokaryote SAG WGS (see S-202, S-203, S-015 and S-016). However, due to the highly variable and generally larger than prokaryote genome sizes of eukaryotes, greater sequencing effort may be needed for a comparable genome fraction to be recovered, in which case the fee for this service depends on the desired sequencing effort.

As with prokaryotes (see above), the fraction of a genome recovered from each eukaryote SAG is variable. Benchmarking of SCGC’s workflow on two marine algae demonstrated high data quality, with the frequency of assembly artifacts that is comparable to those in prokaryote SAGs. However, please note that SPAdes, which we use in de novo assemblies, has not been optimized for diploid organisms. Furthermore, we have not tested the performance of our de novo assembly pipeline on genomes larger than 32 Mbp and therefore cannot guarantee the provision of such assemblies.

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Automated Liquid Handling

Starting at $450.00 per unit

ADDITIONAL SERVICES- SAG re-arraying (S-105)

SAGs are transferred from the original 384-well plates to 96-well plates. The SCGC customer defines transfer volumes, source wells, and destination wells. Prior to the transfer, the destination wells are pre-filled with 5-150 uL of either deionized water or 1x TE buffer, as specified... Show more »

ADDITIONAL SERVICES- SAG re-arraying (S-105)

SAGs are transferred from the original 384-well plates to 96-well plates. The SCGC customer defines transfer volumes, source wells, and destination wells. Prior to the transfer, the destination wells are pre-filled with 5-150 uL of either deionized water or 1x TE buffer, as specified by the SCGC customer. Deliverables include re-arrayed SAGs in a 96-well plate.

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Automated liquid handler

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Cryopreservation

Starting at $100.00 per unit

ADDITIONAL SERVICES- Sample Cryoprotectant glyTE (S-019)

For SCGC customers’ convenience, we offer the preparation and shipment of SCGC’s recommended sample cryoprotectant glyTE. Deliverables of this service include preparation and shipment of 10 mL of 10x concentrated glyTE.

ADDITIONAL SERVICES- Sample Cryoprotectant glyTE (S-019)

For SCGC customers’ convenience, we offer the preparation and shipment of SCGC’s recommended sample cryoprotectant glyTE. Deliverables of this service include preparation and shipment of 10 mL of 10x concentrated glyTE.

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-80 Freezer cryoprotection

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Genomics Consulting

Price on request

ADDITIONAL SERVICES- Consultation (S-011)

Basic support is included in the pricing of all SCGC services. When SCGC customers require more extensive help with study design and/or data interpretation (greater than two hours per project), we may request compensation for the associated labor costs via collaborative research grants... Show more »

ADDITIONAL SERVICES- Consultation (S-011)

Basic support is included in the pricing of all SCGC services. When SCGC customers require more extensive help with study design and/or data interpretation (greater than two hours per project), we may request compensation for the associated labor costs via collaborative research grants or consultant fees. We may also request co-authorship on resulting publications for those SCGC scientists who are providing substantial, project-specific intellectual input.

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User Research

Price on request

ADDITIONAL SERVICES- Customized Services (S-100)

SCGC offers a wide range of customized services, e.g., non-standard cell sorting, non-SAG sequencing, bioinformatics support, method development, etc. Co-authorship on resulting publications may be requested for those SCGC scientists who are providing substantial,... Show more »

ADDITIONAL SERVICES- Customized Services (S-100)

SCGC offers a wide range of customized services, e.g., non-standard cell sorting, non-SAG sequencing, bioinformatics support, method development, etc. Co-authorship on resulting publications may be requested for those SCGC scientists who are providing substantial, project-specific intellectual input. For more information, please contact SCGC manager Brian Thompson.

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PCR Bioinformatics pipelines Bioinformatics

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Cryostorage and Cryoprocessing

Price on request

Cryostorage Services

Cryostorage Services

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DNA Sequencing

Price on request
Request a quote for more information about this service.

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DNA Amplification

Price on request
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Large-Scale DNA Sequencing

Price on request
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Deep Sequencing

Price on request
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Illumina MiSeq Sequencing

Price on request
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Virus Sequencing

Price on request
Request a quote for more information about this service.

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Illumina NextSeq Sequencing

Price on request
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Small Genome Sequencing

Price on request
Request a quote for more information about this service.

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RS

Ramunas Stepanauskas

SCGC Director
BT

Brian Thompson

SCGC Manager

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